something similar happened to me a long time ago. my boyfriend and i never use condoms, but when we did once, the next day, everytime i peed, it burned. but it went away, and i'm fine now.
I also say when in doubt, and everything turns up negative, especially if you're having any burning with urination, to get a HSV test, ask your gyno.
Get your urine tested for bladder infection. Get your cervix tested for cervical infection. Get evaluated by a gynecologist. If these are all negative for pathology, get an evaluation from a qualified pelvic floor physical therapist. You may have pelvic muscle trigger points, which could also cause these symptoms.